I use a Mac, you use a Mac. Our close window button is in the top left corner of the window so it’s convenient when a JavaScript pop-over puts the “button” there, though most don’t. A few I run into I’ve decided to throw some CSS at to fix them.

/**** Mac ready "close" widget ****/
/* WordPress admin "More info..." */
div#TB_ajaxWindowTitle {
position:absolute;
top:0px;
left:25px;
float:none !important;
display:inline !important;
}
div#TB_closeAjaxWindow {
display:inline !important;
float:left !important;
clear:left !important;
}
/* Amazon */
div.ap_close {
left: 24px !important;
}
span.ap_closebutton {
float:left;
clear:left;
}
/* "Fancybox" */
a#fancybox-close {
left:-15px !important;
}
/* "MultiBox" */
div.MultiBoxClose {
left:-26px !important;
}
/* Disqus profile */
a.dsq-modal-close-btn {
position:absolute !important;
top:10px !important;
left:10px !important;
}

This would of course go into your user defined CSS file. Which in Safari can be added at Safari > Preferences | Advanced – Style sheet: